Released in Japan on April 28, 2004, Xenosaga Freaks contained four separate parts: Xeno Komi, which plays like an illustrated, voiced text adventure, a word game called Xeno-pittan, an encyclopedia of Episode I terms, and a playable demo version of Episode II. The Xeno Komi scenario is credited to Yanesaka Norihiko and it was directed by Yuki Mitsuhiro. Though uncredited, some of the music scored by Yasunori Mitsuda for Episode I was used in the game.
Xeno Komi is of interest for the Xenosaga series after Episode III revealed in its database that the events that occurred in Xeno Komi are part of Xenosaga's history. Set sometime during Episode I, Xeno Komi follows the usually humorous intertwining adventures of the six major characters from Episode I and Allen. The main plot involved the seeming unexplained rampage of a cat-ear wearing KOS-MOS as she destroyed significant portions of the Durandal and the Elsa while chasing an imaginary cat. After playing through the scenarios for the six major characters, Allen's scenario is unlocked. His story reveals the events that lead to KOS-MOS' going out of control. Professor and Assistant Scott cornered Allen and after dubbing him Assistant #2, convinced him to help them install a remote control device on KOS-MOS (who has been named Assistant #3). The program to accomplish this was called Schrödinger and the cat-ears that were installed on KOS-MOS were actually antennae.
Other notable Xeno Komi events that foreshadowed Episode II or referenced other Xenosaga side stories included a nightmare Ziggy had of Sharon and Joaquin Rozas after KOS-MOS knocked him unconscious and MOMO briefly meeting Rubedo and Sakura in her subconscious domain.
Xenosaga Freaks was never released in North America and Europe, and currently there is no English translation for it.